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(-) Description

Title :  CRYSTAL STRUCTURE OF QUINOLINIC ACID PHOSPHORIBOSYLTRANSFERASE FROM HELICOBACTER PYLORI
 
Authors :  M. K. Kim, Y. J. Im, J. H. Lee, S. H. Eom
Date :  05 Oct 05  (Deposition) - 14 Feb 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Quinolinate Phosphoribosyltransferase, Quinolinic Acid, Helicobacter Pylori, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Kim, Y. J. Im, J. H. Lee, S. H. Eom
Crystal Structure Of Quinolinic Acid Phosphoribosyltransferase From Helicobacter Pylori
Proteins V. 63 252 2006
PubMed-ID: 16419067  |  Reference-DOI: 10.1002/PROT.20834

(-) Compounds

Molecule 1 - PROBABLE NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: QUINOLINATE PHOSPHORIBOSYLTRANSFERASE, DECARBOXYLATING, QAPRTASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PHT3Ligand/IonPHTHALIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PHT6Ligand/IonPHTHALIC ACID
2SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:126 , GLY A:236 , ASN A:237 , VAL A:256 , GLY A:257 , ALA A:258 , HIS A:261BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWARELYS B:126 , ASN B:237 , GLY B:257 , ALA B:258 , HIS B:261BINDING SITE FOR RESIDUE SO4 B 2002
3AC3SOFTWARELYS C:126 , ASN C:237 , GLY C:257 , ALA C:258 , HIS C:261BINDING SITE FOR RESIDUE SO4 C 2003
4AC4SOFTWARETHR A:124 , ARG A:125 , HIS A:147 , ARG A:148 , MET A:156 , MET A:207 , GLU A:233 , HOH A:2003 , ARG B:91BINDING SITE FOR RESIDUE PHT A 1001
5AC5SOFTWAREARG A:91 , THR B:124 , ARG B:125 , ARG B:148 , MET B:156 , LYS B:158 , MET B:207 , HOH B:2010BINDING SITE FOR RESIDUE PHT B 1002
6AC6SOFTWAREARG C:91 , THR C:124 , ARG C:125 , HIS C:147 , ARG C:148 , LYS C:158 , GLU C:233 , HOH C:2015BINDING SITE FOR RESIDUE PHT C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B7P)

(-) Exons   (0, 0)

(no "Exon" information available for 2B7P)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:273
 aligned with NADC_HELPY | O25909 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
           NADC_HELPY     1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
               SCOP domains d2b7pa1 A:1-102 automated matches                                                                     d2b7pa2 A:103-273 automated matches                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2b7pA02 A:117-262 Aldolase class I                                                                                                                ----------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhh....eeeeeeee...ee..hhhhhhhhhhhh..eeeee.....ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhh...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee......hhhhhhh....eee.hhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7p A   1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with NADC_HELPY | O25909 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
           NADC_HELPY     1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
               SCOP domains d2b7pb1 B:1-102 automated matches                                                                     d2b7pb2 B:103-273 automated matches                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2b7pB02 B:117-262 Aldolase class I                                                                                                                ----------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh.eeeee.....ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhh.............eeehhhhhh...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee......hhhhhhh....eee.hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7p B   1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   


Chain C from PDB  Type:PROTEIN  Length:273
 aligned with NADC_HELPY | O25909 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
           NADC_HELPY     1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
               SCOP domains d2b7pc1 C:1-102 automated matches                                                                     d2b7pc2 C:103-273 automated matches                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2b7pC02 C:117-262 Aldolase class I                                                                                                                ----------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhh....eeeeeeee...ee..hhhhhhhhhhh...eeeee.....ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhh.............eeehhhhhh....hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....eee........hhhhhhh....eee.hhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7p C   1 MEIRTFLERALKEDLGHGDLFERVLEKDFKATAFVRAKQEGVFSGEKYALELLEMTGIECVQTIKDKERFKPKDALMEIRGDFSMLLKVERTLLNLLQHSSGIATLTSRFVEALNSHKVRLLDTRKTRPLLRIFEKYSVLNGGASNHRLGLDDALMLKDTHLRHVKDLKSFLTHARKNLPFTAKIEIECESFEEAKNAMNAGADIVMCDNLSVLETKEIAAYRDAHYPFVLLEASGNISLESINAYAKSGVDAISVGALIHQATFIDMHMKMA 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7P)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NADC_HELPY | O25909)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004514    nicotinate-nucleotide diphosphorylase (carboxylating) activity    Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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  2.4.2.19
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NADC_HELPY | O25909: 2b7n 2b7q

(-) Related Entries Specified in the PDB File

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